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At least 19 recordsLinked to original sources
PubMed1995

The use of the AMBER force field in conformational analysis of carbohydrate molecules: determination of the solution conformation of methyl alpha-lactoside by NMR spectroscopy, assisted by molecular mechanics and dynamics calculations.

The solution conformation of methyl alpha-lactoside has been studied through nmr spectroscopy and molecular mechanics calculations using the assisted model building with energy refinement (AMBER) force field. The nmr data have included nuclear Overhauser effect (NOE) measurements both in the laboratory and rotating frames, longitudinal relaxation times, and homonuclear and heteronuclear coupling constants. The steady-state and transient NOEs have been interpreted in terms of an ensemble average distribution of conformers, making use of the complete relaxation matrix approach. The molecular mechanics calculations have been performed at two dielectric constants [epsilon = 1*r and 80 Debyes (D)] in an exhaustive way, and have been complemented with specific calculations at intermediate epsilon values. Relaxed energy maps and adiabatic surfaces have been generated for the different dielectric constants. The probability distribution of conformers has been estimated from these steric energy maps. Molecular dynamics simulations in vacuo have also been performed. The experimental results indicate that the beta (1-->4)-glycosidic linkage shows some fluctuations among three low energy regions, although spends ca. 85% of its time in the region close to the global minimum. It is shown that the overestimation of the electrostatic contributions in AMBER is responsible for the failure of this force field to explain the experimental results when used at low dielectric constant (epsilon < 20 D). The matching between the expected and observed facts increases for epsilon > 40 D. Different conditions have been tested to perform temperature constant molecular dynamics simulations in vacuo, which have indicated that, when used without explicit solvent, this force field should only be employed in a qualitatively way when analyzing dynamical properties of oligosaccharides.

Carbohydrate Conformation↗
PubMed1991

Carbohydrate-induced conformational changes strongly modulate the antigenicity of coronavirus TGEV glycoproteins S and M.

The carbohydrate composition and the immunoreactivity of the S and M glycoproteins of the coronavirus TGEV were studied at different stages of their maturation. The biosynthesis of S and M was analyzed in the presence of tunicamycin and monensin. The effect of treatment with endoglycosidases H and F and glycopeptidase F on the precursors and mature forms of S and M were also examined. Species 175K and 29K were characterized as high mannose forms of S and M, respectively, and species 220K and 30-36K as complex type glycosylated forms of these two proteins. M was present mainly as a 29K species in mature virions whereas the 175K form of S was not detected, thus implying that the two proteins undergo Golgi modifications at a far different efficiency. Anti-S and -M monoclonal antibodies were examined for their reactivity towards polypeptide species either treated with endo H or produced in the presence of tunicamycin. It was found that (i) among the four major antigenic sites previously defined (Delmas et al., 1986), only site C (amino acids 363 to 371) was notably expressed by the unglycosylated S polypeptide 155K, whereas the three other sites were dependent upon core-glycosylation, (ii) three of the four anti-M mAbs tested did not recognize the unglycosylated M polypeptide 26K. These data led us to conclude that co-translational, but not terminal glycosylation is an essential requirement for both acquisition and maintenance of the antigenicity of TGEV glycoproteins.

Animals↗
PubMed1995

Conformational analysis of carbohydrates inferred from NMR spectroscopy and molecular modeling. Applications to the behavior of oligo-galactomannan chains.

In both the biological functions and industrial applications of carbohydrates, their conformational behavior along with the dynamic fluctuations that their structures experience are of great significance. The elucidation of the three-dimensional characteristics of carbohydrates and carbohydrate-containing molecules is in general performed by a combination of high-resolution nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. Heteronuclear couplings and nuclear Overhauser effect (NOE) data are major tools for structural determination. The angular dependence of carbon-proton coupling constants has been shown to depend also on the pathways involved. Concerning molecular modeling, the goal is to generate the ensemble of structures that are consistent with the experimental data. This approach is illustrated in the galactomannan chain. It consists of the conformational study of two model disaccharides (mannobiose and epimelibiose) of galactomannans through carbon-proton coupling constants and NOE measurements. Experimental data are then compared to results of conformational analysis that predicted the stable conformers in solution. From these results helical conformations of oligomers are generated and are discussed in terms of the influence of the position and number of galactose units on the conformation of the mannan backbone.

Carbohydrates↗
PubMed1977

Carbon-13 as a tool for the study of carbohydrate structures, conformations and interactions.

The application of 13C-NMR spectroscopy to problems involving the structures and interactions of carbohydrates is described. Both 13C-enriched and natural abundance compounds were used and some advantages of the use of the stable isotope are described. Carbon-carbon and carbon-proton coupling constants obtained from 1-13C enriched carbohydrates were employed in the assignment of their chemical shifts and to establish solution conformation. In all cases studied thus far, C-3 couples to C-1 only in the beta-anomers while C-5 couples to C-1 only in the alpha-anomers. C-6 and C-2 always couple to C-1 in both anomeric species. The alkaline degradation of glucose [1-13C] to saccharinic acids was followed by 13C-NMR. The conversion of glucose [1-13C] to fructose-1, 6-bisphosphate [1, 6-13C] by enzymes of the glycolytic pathway was shown as an example of the use of 13C-enriched carbohydrates to elucidate biochemical pathways. In a large number of glycosyl phosphates the 31P to H-1 and 31P to C-2 coupling constants demonstrate that in the preferred conformation and phosphate group lies between the O-5 and the H-1 of the pyranose ring. The influence of paramagnetic Mn2 + ions on the proton decoupled 13C-NMR spectra of uridine diphosphate N-acetylglucosamine indicates that the Mn2 + interacts strongly with the pyrophosphate moiety and with the carbonyl groups of the uracil and N-acetyl groups.

Carbohydrates↗
PubMed1990

[Conformation analysis of carbohydrate chains of glycoconjugates].

A problem of conformations of carbohydrate chains of glycoconjugates-glycoproteins and glycolipids--is reviewed. Experimental data (NMR, X-Ray) and theoretical conformational analysis data are discussed. Spatial structures of O-linked oligosaccharides from blood-group glycoproteins, N-linked oligosaccharides of different types (oligomannosidic, complex, hybrid, bisect) and carbohydrate chains of glycosphingolipids are considered.

Carbohydrate Conformation↗
PubMedDate not supplied

[Segmental flexibility of Fc-region of spin labeled 2 subclasses of IgG molecule from cow blood and local conformational mobility of their carbohydrate components].

Spin-label was bound to carbohydrates of Fc-region of two subclasses of the IgG molecule from the blood serum of healthy and ill cows. By the value of rotational correlation time (10 nsec) internal flexibility of Fc-region of both IgG subclasses and by value of the order parameter (S = 0.9)--rigid attachment of oligosaccharide chains to protein parts of the molecules were found. At the same time the states of IgG1 an IgG2 molecules determined by dynamic steric characteristics for ill and healthy cows did not differ.

Animals↗
PubMed1994

Vibrational Raman optical activity of glycoproteins.

This paper reports the first vibrational Raman optical activity (ROA) spectrum of a glycoprotein. The sample, orosomucoid (alpha 1-acid glycoprotein), shows ROA bands characteristic of a high beta-sheet content together with new bands which could be specific for the carbohydrate and its association with the protein. Our results suggest that ROA spectra of intact glycoproteins may contain information about both protein and carbohydrate conformation and the mutual influence on each other's stability and conformation.

Carbohydrate Conformation↗
PubMed1995

The use of CVFF and CFF91 force fields in conformational analysis of carbohydrate molecules. Comparison with AMBER molecular mechanics and dynamics calculations for methyl alpha-lactoside.

The solution conformation of methyl alpha-lactoside has been studied through molecular mechanics calculations using the AMBER/Homans, CVFF and CFF91 force fields, and compared to NMR nuclear Overhauser data. Steady-state and transient nuclear Overhauser effects (NOEs) have been interpreted in terms of the ensemble average distribution of conformers. The NOEs have been analysed using the complete relaxation matrix approach for a rigid and isotropic motion model. The molecular mechanics calculations have been performed at two dielectric constants (i.e. epsilon = 1 and 80 debyes, or epsilon = r and 80 debyes) in an exhaustive way, and, in some cases, have been complemented by specific calculations at intermediate epsilon values. Relaxed energy maps and adiabatic surfaces have been generated for the different dielectric constants. The probability distribution of conformers has been estimated from these steric energy maps. Molecular dynamics simulations in vacuo have also been performed. Our results indicate that the beta-(1-->4) glycosidic linkage shows some fluctuations between three low-energy regions, although it spends about 90% of its time in the region close to the global minimum. The observed conformation of methyl alpha-lactoside seems to be closer to that predicted by CVFF, although the AMBER/Homans results are also in qualitative agreement with the experimental data.

Carbohydrate Conformation↗
PubMed1983

[Conformation analysis of carbohydrate chains of group-specific substances].

Theoretical conformational analysis of bi- and three-antennary carbohydrate chains of H-specific group substances has been carried out. It has been shown that O-glycosylating oligosaccharides can form compact Y-shaped structures with effective non-bonded interactions between the antennae residues.

Blood Group Antigens↗
PubMed1995

New triterpenoid saponins, asterbatanoside D and E, from Aster batangensis.

Two new triterpenoid saponins named asterbatanoside D and E have been isolated from Aster batangensis and their structures elucidated as 3-O-beta- D-glucopyranosyl-bayogenin-28-O-beta-D-glucopyranosyl-(1-->6)-beta -D- glucopyranoside and 3-O-6'-acetyl-beta-D-glucopyranosyl-bayogenin-28-O-beta-D- glucopyranosyl-(1-->6)-beta-D-glucopyranoside by means of MS, 1D and 2D NMR techniques (COSY, TOCSY, ROESY, HMQC, and HMBC), and chemical reactions.

Carbohydrate Conformation↗
PubMed1995

Steroid alkaloid glycosides from Solanum robustum.

Solamargine, solasonine, N-hydroxyrobustine and a new glycoalkaloid, N-hydroxysolamargine, has been isolated from the leaves of Solanum robustum, the structure of which has been elucidated as (25R)-3beta-{O-alpha-L-rhamnopyranosyl-(1-->2)-O-[alpha-L- rhamnopyranosyl- (1-->4)]-beta-D-glucopyranosyloxy}-22alphaN- spirosol-5-en-N-ol.

Alkaloids↗